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Genetic alterations in cancer patients, identified by new computational method developed in Barcelona

A new computational method allows the detection, within just a few hours, of the genetic alterations responsible for the formation and progression of cancer tumours. This new method manages to accurately identify almost all types of genetic changes of cancer cells in a simple, quick and precise way. It is also able to identify large-scale chromosome rearrangements, which had been difficult to be detect until this breakthrough. The new method, called SMUFIN, has been developed by the Barcelona Supercomputing Centre and the ICREA (Catalan Institution of Research and Advanced Studies), in collaboration with research groups from Barcelona, Oviedo and Heidelberg. This progress has been published by the prestigious journal 'Nature Biotechnology' and represents a significant step forward towards the personalised treatment of cancer and other illnesses.

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27 October 2014 07:55 PM

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ACN

Barcelona (ACN).- A new computational method enables the detection of the genetic alterations responsible for the formation and progression of cancer tumours within just a few hours. This new method manages to accurately identify almost all types of genetic changes of cancer cells in a simple, quick and precise way. It is also able to identify large-scale chromosome rearrangements, which had been difficult to be detect until this breakthrough. The new method, called SMUFIN (Somatic Mutations Finder), has been developed by the Barcelona Supercomputing Centre and the ICREA (Catalan Institution of Research and Advanced Studies), in collaboration with research groups from the Clínic Hospital, the IDIBAPS research institute and the national Genome analysis Centre (CNAG) – all three based in Barcelona – as well as the Asturias Oncology Institute of the University of Oviedo (IUOPA) and the European Biology Laboratory (EMBL), based in Heidelberg. This progress in cancer diagnosis has been published by the prestigious journal 'Nature Biotechnology'. SMUFIN represents a significant step forward towards the personalised treatment of cancer and other illnesses. The genome analysis of each patient can make diagnoses quicker and more accurate, and it can provide more effective and less aggressive treatments.

A new computational method enables the detection of genetic alterations responsible for the formation and progression of tumours, in a simple, quick and precise way. The SMUFIN method is capable of analysing the complete genome of a tumour and identifying its mutations in just a few hours. Furthermore, it can also identify changes which had previously not been revealed, even using methods which previously had required the use of supercomputers over several weeks. The team that has developed SMUFIN is led by David Torrents, ICREA Research Professor at the Barcelona Supercomputing Center (BSC).

One of SMUFIN’s most significant improvements is the radical change it represents in the method by which genomes are analysed. Until now, identifying mutations responsible for the formation and evolution of tumours had involved comparing genomes taken from the tumour with genomes obtained from healthy cells from the same patient via a human reference genome, which is used as a guide. This lengthy and complex process results in the loss of a considerable amount of information and makes it difficult to identify many mutations which have an impact on the tumour. This analysis is also executed by different computer programmes in succession, each one of which is only capable of detecting certain types of variations.

However, SMUFIN carries out a direct comparison between the healthy cell genome and cells from a tumour in the same patient. It then identifies the location of almost all types of mutations at once, without requiring the use of several programmes. Therefore, the analysis is developed in a much quicker and more complete way.

Advances in the research of aggressive tumours

The article published in the 'Nature Biotechnology' journal explains how SMUFIN is also able to reveal hard-to-detect genetic alterations in aggressive cancer tumours. Using SMUFIN to analyse two types of aggressive cancer samples, a blood tumour (mantle cell lymphoma) and one of the nervous system (paediatric medulloblastoma) has allowed the discovery of almost all the types of mutations occurring in their genomes for the first time and with over 90% accuracy. This includes changes in the organisation of chromosomes. This had not been achieved by the methods used until this breakthrough. Therefore, SMUFIN represents the first step necessary towards understanding how these chromosome changes affect the cancer evolution and aggressiveness.